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1. International Journal of Engineering Research and Development
e-ISSN: 2278-067X, p-ISSN: 2278-800X, www.ijerd.com
Volume 10, Issue 6 (June 2014), PP.26-32
Constructing of Phylogenetic Tree for COX based on sequences
by using ClustalW
Chukka Santhaiah1, Dr.A.Rama Mohan Reddy2
1Research Scholar,C.S.E Department, S.V.University , Tirupati , A.P, INDIA.
2Professor, C.S.E Department, S.V.University , Tirupati , A.P, INDIA.
Abstract:-The phylogenetics development of genus is regularly described as the consequence of random
mutations and expected choice, which gives rise to the perception of phylogenetic trees. The big quantity of
soaring excellence sequence data accessible has ended the rebuilding of phylogenetic trees as of sequence data
achievable. In this work COX gene is taken from NCBI P22437.1 as a protein with its accession number. The
Clustal approach is a influential and admired alternative for create phylogenetic trees as of sequence data, no
limit in the size of the trees, which can be constructed. The aim of work is speed up tree reconstruction by
construction use of preceding information. Here put forward a new heuristic for incorporating a phylogenetic
tree for protein datasets are converted to DNA datasets and construct the phylogenetic tree for analogous data
set. In this work we implement the proposed Clustal for multiple alignments. The experiments performed show,
which incorporating prior knowledge leads to a significant speed up, if large amounts are included.
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Keywords:- Clustal, DNA, Protein, Phylogenetic tree
I. INTRODUCTION
Phylogenetics is the cram of development affairs linking organisms. Expertise has permit astonishing
evolution in phylogenetics. One portion of this in the biology itself. The innovation of DNA and the capability
for biologists to sequence DNA has, to say the slightest revolutionized the field. Computers have assisted
extremely as well. To the side from their relieve in sequencing assignments, computers smooth the progress of a
broad array of phylogenetic problem-solving activities.
The contribution of computers (or perhaps more appropriately, computer science) is text processing.
Since DNA sequences come as a sequence of characters (from the alphabet A, C, T, G), there are several
computer science algorithms that can be used as processing tools. The field of phylogenetics has applications to
molecular biology, genetics, evolution, epidemiology, ecology, conservation biology, and forensics to name a
few. Phylogenies are the chronological and evolutionary relationships among organisms. Researchers can
employ this data to better understand how viruses spread or to study common biological processes between
different species of life.
Cyclooxygenase also known as Prostaglandin endoperoxide H synthase (PGHS, EC.1.14.99.1) and
exists in two isoforms; (COX-1) and (COX-2), which catalyses the oxidation of AA to prostanoids. COX-1 and
COX-2 enzymes are heme proteins, homodimers that are widely distributed. These enzymes are located in the
lumenal portion of the endoplasmic reticulum membrane and the nuclear envelope [1]. Cox isoenzymes are also
involved in a wide range of pathologies that include for Cox-1 thrombosis, and for Cox-2 inflammation, pain
and fever, various cancers, and neurological disorders like Alzheimer’s and Parkinson’s diseases [2]. Big
success was achieved with the development of non-steroidal anti-inflammatory drugs (NSAIDs) such as aspirin
for treatment of fever and pain [3].
A multiple sequence alignment (MSA) is a sequence alignment of three or more biological sequences
such as protein, DNA, or RNA. Typically it is implied that the set of equences share an evolutionary
relationship, which means they are all descendents from a common ancestor. These regions may correspond to
functional, structural, or evolutionary relationships between the sequences. Alignments can reflect a degree of
evolutionary change between sequences that are descendants from a common ancestor. There is a relationship
between phylogenies and sequence alignments [4].
There are various techniques used to create phylogenetic trees and most of them rely on aligned genetic
sequences to perform this task. Probably the most popular genetic sequence alignment algorithm is ClustalW
[4]. Although successful in its domain, ClustalW is very sensitive to highly divergent sequences. Therefore the
purpose of this project is to modify the ClustalW sequence alignment algorithm so that it can be used to
construct a more accurate tree when highly divergent sequences are present. Sequence alignment is a way of
arranging sequences of DNA, RNA, or proteins in order to distinguish regions of similarity. ClustalW is a
popular program used for multiple sequence alignment and for preparing phylogenetic trees. Its portability
amongst various computing platforms is the main reason for its widespread use. Due to its popularity and the

2. Constructing of Phylogenetic Tree for COX based on sequences by using ClustalW
availability of source code, ClustalW was used for this project. The progressive alignment algorithm used by
ClustalW to perform a multiple sequence alignment [5].
II. METHODOLOGY
The methodology purpose is to get the nucleotide sequences by using protein sequences that are related
to same sequences. In this process first select the one protein that is main protein for entire this process. Here
that protein P22437.1. It is a protein that is related to COX gene of the one family. To get the nucleotide
sequence from amino acid sequence by performing different operations on selected protein. The methodology
follows different operations.
a. Search the protein form database that is related to COX.
b. Give that protein in the NCBI database for find the sequence in the form of FASTA [6].
c. Then select the FASTA format of protein and paste the in BLAST for BLAST operation of
tBLASTn. It takes some time for execution based on sequence length [7].
d. The output is gives graphic summary and description of gene. And it displays related genes.
e. In output contains the gene description of the related name of genes, maximum score, total score
identity of genes and accession number of that genes.
f. Based on gene accession number to find the nucleotide sequences from protein sequences.
g. Then select the all sequences, copy the FASTA format of the sequences and paste in ms-word
27
format for ClustalW operation.
h. Finally perform the ClustalW operation and it provides rooted and Unrooted phylogenetic tree [8].
In the above operations we get the nucleotide sequence from amino acid sequence, and also to create the
phyologenetic tree based on nucleotide sequences. To get the phylogenetic tree with the help of DNA sequences.
The output file contain rooted and unrooted phylogenetic tree. In phylogenetic tree the similar sequences are
form as taxa. The remaining sequences are grouped as a whole tree of similar tree. The execution of the
nucleotide process may take few seconds/minutes based on sequence length, processor and internet speed.
III. RESULTS
1. Cox1 Protein sequence
>gi|129900|sp|P22437.1|PGH1_MOUSE RecName: Full=Prostaglandin G/H synthase 1; AltName:
Full=Cyclooxygenase-1; Short=COX-1; AltName: Full=Prostaglandin H2 synthase 1; Short=PGH synthase 1;
Short=PGHS-1; Short=PHS 1; AltName: Full=Prostaglandin-endoperoxide synthase 1; Flags: Precursor
MSRRSLSLWFPLLLLLLLPPTPSVLLADPGVPSPVNPCCYYPCQNQGVCVRFGLDNYQCDCTRTGYSGP
NCTIPEIWTWLRNSLRPSPSFTHFLLTHGYWLWEFVNATFIREVLMRLVLTVRSNLIPSPPTYNSAHDYIS
WESFSNVSYYTRILPSVPKDCPTPMGTKGKKQLPDVQLLAQQLLLRREFIPAPQGTNILFAFFAQHFTHQ

3. Constructing of Phylogenetic Tree for COX based on sequences by using ClustalW
FFKTSGKMGPGFTKALGHGVDLGHIYGDNLERQYHLRLFKDGKLKYQVLDGEVYPPSVEQASVLMRY
PPGVPPERQMAVGQEVFGLLPGLMLFSTIWLREHNRVCDLLKEEHPTWDDEQLFQTTRLILIGETIKIVI
EEYVQHLSGYFLQLKFDPELLFRAQFQYRNRIAMEFNHLYHWHPLMPNSFQVGSQEYSYEQFLFNTSM
LVDYGVEALVDAFSRQRAGRIGGGRNFDYHVLHVAVDVIKESREMRLQPFNEYRKRFGLKPYTSFQEL
TGEKEMAAELEELYGDIDALEFYPGLLLEKCQPNSIFGESMIEMGAPFSLKGLLGNPICSPEYWKPSTFG
GDVGFNLVNTASLKKLVCLNTKTCPYVSFRVPDYPGDDGSVLVRRSTEL
Fig 1: The FASTA format of input Protein (P22437.1)
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2. Cox1 Protein sequence tBLASTn results
Fig 2: The graphic Summary of query sequence.

4. Constructing of Phylogenetic Tree for COX based on sequences by using ClustalW
29
ClustalW Results:
Fig 3: The result of ClustalW of input sequences

5. Constructing of Phylogenetic Tree for COX based on sequences by using ClustalW
Fig 4: ClustalW result: Rooted Phylogenetic Tree with branch length (UPGMA) of Cox1
Fig 5: ClustalW result: Rooted Phylogenetic Tree (UPGMA) of Cox1
30

6. Constructing of Phylogenetic Tree for COX based on sequences by using ClustalW
Cox2 Protein sequence
>gi|13487701|gb|AAK27680.1| cyclooxygenase 2 [Mus musculus]
31
XTRQIAGR
Cox2 Protein sequence tBLASTn results
Fig 6: No significant similarity of input sequence (AAK27680.1)

7. Constructing of Phylogenetic Tree for COX based on sequences by using ClustalW
IV. CONCLUSIONS
It has been shown to a great extent curiosity in phylogenetic systematic recently. Since the reason that
it is a technique for biologists to rebuild the pattern of events that have led to the distribution and diversity of
life. Due to the “Tree of Life” proposals, and studies the researchers have tried to find some new methods to
combine large number of trees to construct phylogenies on hundreds, or even thousands of species. For
understanding the language of genes and proteins we have to find a suitable model of how they have evolved in
the course of evolution. Because of this we need to develop tree building methods which discover the process of
evolution. These kinds of methods have gained importance with the advent of molecular biology.
REFERENCES
[1]. J. R. Vane,Y. S. Bakhle1, and R. M. Botting , Annu. Rev. Pharmacol. Toxicol. 1998. 38:97–120,
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Cyclooxygenases 1 and 2
[2]. Garavito RM, Malkowski MG, DeWitt DL. 2002. The structures of prostaglandin endoperoxide H
synthases-1 and -2. Prostaglandins Other Lipid Mediat 68-69:129-52.
[3]. Mag.rer.nat.Kerstin Kitz ,2011,Transcriptional Regulation of Cox-2 Expression in Human
Osteosarcoma cells.
[4]. Higgins,D.G. (1994) CLUSTAL V: multiple alignment of DNA and protein sequences. Methods Mol.
Biol., 25, 307–318
[5]. Thompson, Julie D., Desmond G. Higgins, and Toby J. Gibson. "CLUSTAL W: Improving the
Sensitivity of Progressive Multiple Sequence Alignment Through Sequence Weighting, Position
Specific Gap Penalties and Weight Matrix Choice." Nucleic Acids Research 22 (1994): 4673-4680.
[6]. http://www.ncbi.nlm.nih.gov/
[7]. http://www.ncbi.nlm.nih.gov/tblastn
[8]. http://www.genome.jp/clustalw/